Contacts of the helix formed by residues 268 - 287 (chain B) in PDB entry 4FE1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ASP* 3.6 48.2 - - + -
238B THR 4.2 7.6 - - - -
239B ALA* 4.9 2.0 - - + -
257B LEU* 3.8 24.7 - - + +
258B GLY 3.3 26.8 + - - -
259B GLY 3.9 6.5 + - - -
260B PHE 3.8 10.8 + - - -
261B HIS* 3.8 37.2 - - - -
262B PRO* 3.7 21.5 - - + -
267B LEU* 1.3 75.5 - - - +
269B LEU* 1.3 66.2 + - - +
270B THR* 3.9 11.2 - - - +
271B ASP* 3.1 34.8 + - + +
272B MET* 3.1 15.0 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 3.9 18.8 - - + +
193B LEU* 4.0 14.9 - - + +
197B ALA* 3.5 34.8 - - + +
198B ILE* 3.7 14.5 - - + +
201B SER* 3.4 35.4 - - - +
243B PHE* 3.8 19.0 - - + -
267B LEU 3.5 3.7 + - - +
268B TRP* 1.3 71.2 - - - +
270B THR* 1.3 58.8 + - + +
272B MET* 3.2 24.4 + - + +
273B ALA* 2.9 28.9 + - - +
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Residues in contact with THR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.7 19.3 - - + -
202B ARG* 3.9 11.2 - - - +
236B PRO* 4.8 0.7 - - - +
237B ASP* 4.4 8.9 + - - +
252B ALA* 3.1 34.5 - - + +
253B ILE* 3.7 15.5 - - - +
255B THR* 3.1 27.9 + - - +
257B LEU* 4.5 4.0 - - - +
268B TRP* 3.9 10.2 - - - +
269B LEU* 1.3 77.6 - - + +
271B ASP* 1.3 60.5 + - - +
273B ALA* 3.4 2.5 + - - +
274B HIS* 3.1 22.5 + - - +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B THR* 2.6 35.7 + - - +
256B PHE* 4.3 5.9 - - - -
257B LEU* 3.0 18.0 + - - +
258B GLY* 2.7 31.2 + - - -
259B GLY 5.0 0.3 - - - +
267B LEU* 5.5 1.3 - - + -
268B TRP* 3.1 28.7 + - + +
270B THR* 1.3 79.1 + - - +
272B MET* 1.3 59.6 + - + +
274B HIS* 3.3 5.4 + - - +
275B HIS* 3.0 25.5 + - - +
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Residues in contact with MET 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 4.7 4.7 - - + -
193B LEU* 4.1 9.6 - - + -
267B LEU* 3.6 44.0 - - + +
268B TRP 3.1 18.7 + - - +
269B LEU* 3.2 30.7 + - + +
271B ASP* 1.3 77.6 - - + +
273B ALA* 1.3 65.3 + - - +
275B HIS* 3.2 9.6 - - + +
276B HIS* 3.0 38.2 + - + +
360B PRO* 4.0 26.0 - - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA* 4.0 6.8 - - - +
193B LEU* 3.8 24.6 - - + +
194B ILE* 4.0 19.1 - - + -
198B ILE* 4.3 2.9 - - + -
253B ILE 3.8 14.8 - - - +
254B LEU* 4.0 2.2 - - - -
269B LEU 2.9 15.5 + - - +
270B THR 3.7 4.9 - - - +
272B MET* 1.3 74.7 - - - +
274B HIS* 1.3 66.9 + - - +
276B HIS* 3.2 4.7 + - - +
277B LEU* 3.0 22.3 + - - +
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.4 30.8 - - + +
255B THR* 3.2 31.1 + - - +
256B PHE* 4.7 18.2 - + + -
270B THR 3.1 11.0 + - - +
271B ASP 3.3 4.9 + - - +
273B ALA* 1.3 75.1 - - - +
275B HIS* 1.3 64.1 + - - +
277B LEU* 3.1 10.6 + - + +
278B ALA* 2.9 32.6 + - + +
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ASP 3.0 14.4 + - - +
272B MET* 3.2 12.8 - - + +
273B ALA 3.1 0.2 - - - -
274B HIS* 1.3 77.1 - - - +
276B HIS* 1.3 93.3 + + - +
278B ALA* 3.4 4.6 + - - +
279B ILE* 3.0 49.0 + - + +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 2.9 39.9 + - - +
189B TRP* 3.6 34.4 - + + -
190B ALA* 4.2 8.5 - - + +
193B LEU* 4.0 4.2 - - + +
272B MET* 3.0 34.0 + - + +
273B ALA 3.9 3.8 - - - +
275B HIS* 1.3 96.5 + + - +
277B LEU* 1.3 57.9 + - - +
279B ILE* 4.1 2.9 - - + -
280B ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LEU* 3.8 27.1 - - + -
190B ALA* 3.9 12.5 - - + +
194B ILE* 5.3 3.6 - - + -
254B LEU* 3.7 34.5 - - + -
273B ALA 3.0 13.6 + - - +
274B HIS* 3.1 15.2 + - + +
276B HIS* 1.3 76.8 - - - +
278B ALA* 1.3 62.4 + - - +
280B ALA* 3.4 17.1 - - + +
281B VAL* 3.5 15.1 + - + +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B HIS* 2.9 25.3 + - + +
275B HIS* 3.8 5.4 - - - +
277B LEU* 1.3 72.9 - - - +
279B ILE* 1.3 69.1 + - + +
281B VAL* 3.0 19.8 + - - +
282B LEU* 3.1 18.7 + - + +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 3.1 21.8 - - - +
275B HIS* 3.0 44.5 + - + +
276B HIS* 3.6 5.2 - - + +
278B ALA* 1.3 79.2 - - + +
280B ALA* 1.3 60.1 + - - +
282B LEU* 3.2 13.9 + - + +
283B PHE* 3.0 57.3 + - + -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLY* 3.5 26.0 - - - +
186B SER* 4.2 3.6 - - - -
187B LEU* 3.6 25.8 - - + +
276B HIS 2.9 14.1 + - - +
277B LEU* 3.4 12.3 - - + +
279B ILE* 1.3 77.3 - - - +
281B VAL* 1.3 57.1 + - + +
283B PHE* 3.2 2.8 + - - +
284B ILE* 2.9 38.1 + - + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.8 16.6 - - + +
278B ALA* 3.0 11.2 + - - +
280B ALA* 1.3 76.1 - - + +
282B LEU* 1.3 73.7 + - + +
284B ILE* 3.3 7.3 + - + +
285B VAL* 3.0 35.6 + - + +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ALA* 3.1 15.5 + - + +
279B ILE* 3.2 17.7 + - + +
281B VAL* 1.3 87.9 - - + +
283B PHE* 1.3 64.5 + - + +
285B VAL* 3.4 9.2 + - + +
286B ALA* 3.0 26.9 + - - +
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU* 3.1 30.6 - - + +
179B ALA* 3.4 6.9 - - - -
182B PHE* 3.4 44.6 - + + -
183B GLY* 3.6 9.6 - - - -
186B SER* 5.3 0.4 - - - -
279B ILE* 3.0 51.5 + - + +
282B LEU* 1.3 76.8 - - + +
284B ILE* 1.3 59.9 + - - +
285B VAL 3.1 1.8 - - - -
286B ALA* 3.2 7.7 + - + +
287B GLY 2.9 24.4 + - - -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ALA* 3.8 25.8 - - + +
183B GLY* 4.0 7.2 - - - -
184B VAL* 4.4 17.0 - - + -
187B LEU* 4.5 17.5 - - + -
280B ALA* 2.9 26.6 + - + +
281B VAL* 3.9 6.5 - - - +
283B PHE* 1.3 73.4 - - - +
285B VAL* 1.3 55.0 - - + +
287B GLY 3.4 4.2 + - - -
288B HIS* 2.4 50.8 + - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B VAL* 3.0 32.1 + - + +
282B LEU* 3.5 9.2 - - + +
284B ILE* 1.3 80.0 - - + +
286B ALA* 1.3 59.2 + - - +
288B HIS* 2.9 32.6 + - + +
289B MET* 4.9 0.3 - - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASN* 4.5 1.4 - - - +
178B LEU* 3.9 26.2 - - + +
282B LEU 3.0 16.9 + - - +
283B PHE* 3.2 12.1 + - + +
285B VAL* 1.3 78.0 - - - +
287B GLY* 1.3 56.7 + - - +
288B HIS 2.9 4.6 + - - -
289B MET* 3.1 28.7 + - - +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASN* 3.2 48.5 + - - +
178B LEU* 4.0 3.6 - - - +
179B ALA* 3.5 18.4 - - - +
283B PHE 2.9 10.1 + - - -
284B ILE 3.4 0.2 + - - -
285B VAL 3.1 1.0 - - - -
286B ALA* 1.3 74.4 - - - +
288B HIS* 1.3 64.8 + - - +
289B MET 3.3 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il